Three pygmy killer whales have died after a small pod was stranded onshore at a Northland beach overnight, less than a day after another stranded whale died.

Four whales were found on Waipu beach about 6pm Monday and reported to Project Jonah and the Department of Conservation. One of the pygmy whales had to be euthanised on Monday night, with two more following close to eleven on Tuesday morning as they were too ill to be saved. The fourth whale is still believed to have been successfully re-floated and in the ocean.

DoC spokeswoman Abi Monteith said local iwi will now decide what to do with the whales. They will either be cleansed, buried or passed on for scientific research.

Earlier on Tuesday morning, Monteith said they had a reasonable expectation that the whales would become stranded again. As predicted, two of the whales were found on the same beach, although they were stranded at opposite ends.

Monteith said a group of surf life savers and volunteers were looking after them and no more help was needed.

"The situation is continually changing at the moment and the fourth whale hasn't been found. We are still making assessments on the situation."

Project Jonah spokesperson Daren Grover said there were several people with the whales last night when they first got a phone call about the stranding.

Pygmy killer whales are very small, he said, normally around two-and-a-half metres long. This meant members of the public were able to keep the whales from fully stranding before Project Jonah first arrived, he said.

"At the moment the situation is under control, there are Massey University scientists here and the whales are being monitored and assessed constantly."

Grover said the whales came in with high tide, around 8am, and are now lying further up the beach than last night.

Less than 12 hours earlier on Monday morning, just after high tide, a beaked whale was found at Moureeses Bay in Northland.